3Rad Demultiplexing

Hi there,

I have a dataset of 3Rad data, which have been created by using two pairs of enzymes (pstI/mspI and NsiI/MspI). I used to use Stacks but I now realize it only allows a maximum of 2 enzymes in process radtags. Does anyone know of an other tool or a way to pass by this problem? My first thought was to do 2 consecutive runs in process radtags, one for each pairs, but I’m afraid it will leave residues in my dataset.

Thank you!

Hi @Joelle99,
I checked the Stacks documentation, and I think that it is not possible to provide three enzymes as input.

Regards

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Thank you for the reply! In the end, I think you were right so I changed the way I worked. I decided to use only two of my enzymes (one common and the rare cutter) but activated the “Disable checking if the RAD site is intact” in Stacks V2.55, under “advanced option” after you enter the enzymes. That way, it seems the restriction enzymes didn’t matter much and I limited the loose of sequences due to this.

Hope it helps someone else that might have the same problem!

Regards

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